Does the clipping of nails nullify ablution?
No, it does not, and it is preferable to wash the hands afterwards.
How do I deal with whispers (waswasa) in ablution and purification?
Whispers in ablution are from Satan, and the Muslim should not pay attention to them. He is not required to re-perform ablution or repeat washing a limb because of waswasa. He should always base his purification on its being valid. It is recommended for him to frequently say "La ilaha illa Allah" (There is no god but Allah), because Satan recoils when Allah is mentioned. And Allah the Almighty knows best.
What is the ruling on istinja' after urination, and is it done with water and soap or with water only?
Istinja' from urine and stool is obligatory. It is permissible to perform istinja' with water alone, or with toilet paper alone. The best way is with toilet paper then water. If one wishes to suffice with one of them, then water is better. And Allah the Almighty knows best.
If a woman becomes pure from menstruation before the Fajr Adhan in Ramadan, is she required to fast?
If a woman becomes pure (from menstrual period) before the Fajr Adhan, she must fast, as the impediment preventing her from fasting has been removed. The Sharia maxim in this regard states: "When the impediment is removed, the obligation returns."
She should then make the intention to fast before Fajr and perform ghusl (ritual purification) for prayer, whether before or after Fajr.